Genomic characterisation of a Proteus mirabilis clinical isolate from China carrying blaNDM-5 on an IncX3 plasmid.

Abstract

Acquisition of carbapenemases is of particular concern in Proteus mirabilis, which is intrinsically resistant to tigecycline and colistin, as it makes clinical therapy extremely difficult. Here we report the whole genome sequence of a P. mirabilis clinical isolate from China (CRPM10) harbouring blaNDM-5 on an IncX3-type plasmid. Whole-genome sequencing of the isolate was performed using an Illumina HiSeqTM 4000 platform and MinION sequencer. Hybrid assembly of short Illumina reads and long MinION reads was performed using Unicycler v.0.4.7. Functional annotation was performed by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) server, and further genomic analyses were performed. The complete genome sequence of P. mirabilis CRPM10 consisted of a chromosome of 4 158 695 bp and one IncX3-type plasmid of 46 161 bp (pNDM-5). Fourteen antimicrobial resistance genes (ARGs) were identified in CRPM10. The ARGs were all located on the chromosome except for blaNDM-5, which was located on the IncX3-type plasmid pNDM-5. Plasmid sequence alignment of pNDM-5 with the NCBI GenBank database revealed several highly identical plasmids from different Enterobacteriaceae strains. Here we report the complete genome sequence of a P. mirabilis clinical isolate from China carrying blaNDM-5 on an IncX3-type plasmid. The 46 161-bp IncX3-type plasmids may play an important role in the distribution of NDM mutants among Enterobacteriaceae strains. Considering the global emergence of the NDM-5 carbapenemase, an epidemiological survey and analysis of blaNDM-5-harbouring Enterobacteriaceae strains are urgently required to prevent its future prevalence.